Comparative Genomic and Functional Profiling of ECM-Targeting Enzymes in Bacteroides, a Key Genus of the Human Gut Microbiome

Abstract

Purpose The human extracellular matrix (ECM) provides essential cues for intestinal homeostasis. While most studies focus on ECM degradation by host cells, our prior work suggests that commensal gut microbes may also contribute to these remodeling processes. Here, we continue exploring this novel dimension of host-microbe interactions by profiling the proteolytic diversity and substrate-specific activity of ECM-targeting enzymes across species of Bacteroides, a dominant and metabolically versatile gut genus. MethodsWe curated a custom ECM-specific enzyme database from the BRENDA repository and used it to perform comparative genomic analyses across 11 Bacteroides species, mapping the diversity and abundance of candidate ECM-degrading proteases and carbohydrate active enzymes (CAZymes). Functional activity was evaluated via in vitro degradation assays using purified substrates. Family-specific protease inhibitors were used to confirm the major catalytic classes involved. ResultsECM-targeting CAZymes and proteases were broadly encoded across all 11 genomes, with gene counts positively correlated with genome size and GAG-associated genes comprising the largest substrate category. Experimental degradation assays revealed species- and substrate-specific activity patterns, including elastin degradation restricted to a subset of species, a capacity previously undocumented in intestinal Bacteroides. Genomic predictions showed limited concordance with measured enzymatic activity, suggesting context-dependent regulation of ECM-degrading enzymes. Inhibitor experiments confirmed that collagen degradation is driven primarily by metalloproteases and secondarily by serine proteases across representative species. ConclusionsOur findings position commensal Bacteroides as a rich, yet underappreciated, source of ECM-degrading enzymes. This work underscores the need to consider microbiota as key modulators of host tissue homeostasis and potential targets for therapeutic modulation. BIOGRAPHYDr. Ana Maria Porras is an Assistant Professor of Biomedical Engineering at the University of Florida, where she leads the Tissue-Microbe Interactions lab. Her group leverages cell and tissue engineering, bioinformatics, and statistical modeling to understand how microorganisms regulate human extracellular matrix remodeling. Her work centers primarily on the gut microbiome, cardiovascular health, and tropical infectious diseases. Dr. Porras is also a science artist, and a science communicator, particularly in interested in evidence-based, culturally informed, and multilingual practices to improve public engagement with science. She is the co-founder and Senior Advisor of the Latinx in Biomedical Engineering community, and the recipient of multiple awards, including the UF Excellence Award for Assistant Professors, the NSF Faculty Early Career Development (CAREER) Award, the NIH Maximizing Investigators Research Award (MIRA), the AAAS Early Career Award for Public Engagement with Science, and and the Rising Star Award from the Academy of Science, Engineering, and Medicine of Florida. Prior to arriving in Florida, Dr. Porras was a Presidential Postdoctoral Fellow at Cornell University. She holds a B.S. in biomedical engineering from the University of Texas at Austin, and a Ph.D. from the University of Wisconsin-Madison, where she was an American Heart Association Predoctoral Fellow.